^ I for one am perfectly comfortable with the idea that imprecision in language and the occasional misspeak by crew or characters (going uncorrected for whatever reason) probably explains away most of the scientific weirdness on screen.

To get back on topic (not that I mind straying), I've quickly gone through the transcrips on chakoteya.net. Using key word searches like Nacelle, pod, intermix, antimatter, I've collected some key quotes for us to go through.

Now of course some context was omitted from this due to the size, but I wanted to start somewhere. Remember, I just quickly collected this over the past 30 minutes.

Some quotes are stand alone. Some are more then one line of dialogue (no spaces between those sentences).

What I would like to do, is go through them more slowly expanding on key words to include engine, crystal, and power.

SPOCK: Apparently, this double, however different in temperament, has your knowledge of the ship, its crew, its devices. This being the case, perhaps we can outguess him by determining his next move. Knowing how the ship is laid out, where would you go to elude a mass search?
KIRK: The lower levels. The Engineering deck.

[COLOR=#606420]The Apple[/COLOR]
KIRK: Then use your imagination. Tie every ounce of power the ship has into the impulse engines. Discard the warp drive nacelles if you have to, and crack out of there with the main section, but get that ship out of there!
SCOTT: Tractor beam gone. Potency returning to antimatter
KIRK: We'll do the walking, Scotty. You get on the antimatter pod. If it gets worse, let me know, we'll beam up. Kirk out pods.
KIRK: Kirk here.
SCOTT [OC]: Scott, sir. Our antimatter pods are completely inert.

SPOCK: I would say none, Captain. The energy generated by our power nacelles seems to attracts it. I doubt we could manoeuvre close enough without drawing a direct attack upon ourselves.

KIRK: Go.
WASHBURN: We made a complete check on structural and control damage, sir. As far as we can tell, something crashed through the deflectors and knocked out the generators. Somehow the antimatter in the warp drive pods has been deactivated.
KIRK: Deactivated? Scotty, could some kind of general energy dampening field do that, and would the same type of thing account for the heavy subspace interference?

NORMAN: I am in total control of your ship. I have connected the matter-antimatter pods to the main navigational bank. A trigger relay is now in operation. Any attempts to alter course will result in immediate destruction of this vessel.

SPOCK: No doubt about it, Captain. The space debris comes from the survey vessel SS Beagle.
KIRK: Missing for six years, and now this junk in space.
SPOCK: Portions of the antimatter nacelles, personal belongings. Captain, no signs of bodies whatsoever.

Well, the point is this. I was able to find enough references to the nacelles being volitile and energy producing (m/arc). Instances where they would have to be jettisoned. And no references to that same type of energy being produced within the main hull.

There would be no reason to dump the nacelles if they weren't the matter-antimatter generators.

And my favorite quote is where the nacelles are refered to as the matter antimatter nacelles.

Now as I said, I'm going to be more thorough on the weekend, and I challange anyone in the m/arc in the secondary hull camp to do the same.

There would be no reason to dump the nacelles if they weren't the matter-antimatter generators.

Click to expand...

Oh, dunno about that. They are so much dead weight if they are out of commission, after all. In "The Apple", the reference to cutting them loose is combined with the idea of paring down the ship to the essentials in other ways as well, so that the impulse engines have a better chance of saving the "main section".

The only other reference to nacelle jettison, from "The Savage Curtain", may indeed be related to the nacelles being volatile. But "That Which Survives" shows that a singular pod somewhere in the bowels of the ship is the bit to be ejected when antimatter fuel flow cannot be otherwise controlled; "jettison" might refer to antimatter pod jettison in both cases, rather than to the already disengaged warp nacelles.

As for the rest of the "pod" references, none of them indicates an outboard pod explicitly. All could thus tie together (a definite plus in jargon) and refer to the indoors, user-accessible antimatter storage pods of, say, "That Which Survives" fame. In that sense, all of these references support an internal storage arrangement for antimatter.

I copied this from my earlier notes that I referenced at the beginning of the thread. In the notes below, there is evidence for antimatter in the nacelles and a central reactor. I try to use the least amount of Retcons to tie it all together and borrow heavily from ideas that Tin_Man, Mytran and Albertese have put forth. As always, YMMV

Personal Theory (updated with regeneration theory):

The TOS Enterprise is mainly powered by dilithium crystals that are re-charged by it's matter/antimatter reactor system containing 3 reactor cores. The central M/AM reactor core charges the dilithium crystals which generates ("regenerates") antimatter fuel and simultaneously stores energy to be used to power ship's systems through the energizers. The regenerated AM is pumped to fuel the M/AM engines in the nacelles to generate the space warp. Unused M/AM fuel in the nacelles are stored there in temporary fuel pods and excess fuel is pumped back to the main fuel areas in the engineering hull.

It can be explained that all three reactor cores aren't involved in every episode. In "That Which Survives", Losira's sabotage of the engineering hull's M/AM core was enough to have a runaway ship. In "The Savage Curtain", the "red zone" alert could be something that only can happen in the nacelles since the aliens only needed to target something that was vulnerable.
Notes

For example, there is plenty of evidence of a multiple matter-antimatter reactor model that indicates that there is a matter/antimatter reactor and fuel in each nacelle:

"The Doomsday Machine" - 35

WASHBURN: We made a complete check on structural and control damage, sir. As far as we can tell, something crashed through the deflectors and knocked out the generators. Somehow the antimatter in the warp drive pods has been deactivated.
​

Note: Evidence of antimatter in the warp drive pods aka nacelles.

SPOCK: I would say none, Captain. The energy generated by our power nacelles seems to attracts it. I doubt we could manoeuvre close enough without drawing a direct attack upon ourselves.

Note: Since the nacelles generate energy then it's a good chance they have a m/am reactor in them.
​

"The Apple" - 38

SCOTT: Scott, sir. Our antimatter pods are completely inert.

Note: Could the "antimatter pods" = the nacelles? Or is this specific to antimatter pod containing the antimatter fuel?

KIRK: Then use your imagination. Tie every ounce of power the ship has into the impulse engines. Discard the warp drive nacelles if you have to, and crack out of there with the main section, but get that ship out of there!

Note: Nothing specific to M/AM generation here other than the warp drive nacelles are weighing down the ship and they are trying to break out of orbit.
​

SPOCK: There is one other possibility, Mister Scott. The final decision, of course, must be the captain's, but I believe we must have it ready for him. The Enterprise is propelled by matter-anti-matter reactors. The barrier we must traverse is negative energy.

Note: An interesting clue. Multiple matter-antimatter reactors. Perhaps the three reactors spoken of in "Catspaw" (two for each nacelles and one for the engineering hull?) or just two (one for each nacelle)?

SCOTT: I have opened the control valves to the matter-anti-matter nacelles. On your signal, I will flood them with positive energy.

Note: "Matter-antimatter nacelles" - Yes But what is this? Flood the nacelles with positive energy?
​

"The Savage Curtain" - 77

SCOTT: I can't explain it, sir, but the matter and antimatter are in red zone proximity.
KIRK: What caused that?
SCOTT: There's no knowing and there's no stopping it either. The shielding is breaking down. I estimate four hours before it goes completely. Four hours before the ship blows up.
...
KIRK: Scotty, inform Starfleet Command. Disengage nacelles, Jettison if possible. Mister Spock, assist them. Advise and analyse. Scotty? Scotty?

Note: Further evidence that there is matter and antimatter (and it happens to include the fuel) up in the nacelles. And this occurs very late in the production too... episode 77 no less. Interestingly, the Matter is also in the Red Zone? This may point to fuel in only specific locations can go into Red Zone which would explain how Kirk knew that only the nacelles were in trouble.
​

"Errand of Mercy" - 27

SPOCK: Minor, Captain. We were most fortunate. Blast damage in decks ten and eleven, minor buckling in the antimatter pods, casualties very light.
Note: "Antimatter pods" could mean the nacelles or just the pods in the nacelles or antimatter pods located somewhere else...
​

"Metamorphosis" - 31

SPOCK: Helm does not answer, Captain.
KIRK: Neither do the pods. Communications are dead. Building overload. Cut all power relays.
...
SULU: Steady. No, Mister Scott, bearing three ten mark thirty five just cleared. No antimatter residue.
SCOTT: All scanners, spherical sweep. Range, maximum. They'll have to pick it up.

Note: This is shuttlecraft-related but this also hints that those were antimatter pods and thus an antimatter-powered shuttle at the minimum.
​

"I, Mudd" - 41

NORMAN: I am in total control of your ship. I have connected the matter-antimatter pods to the main navigational bank. A trigger relay is now in operation. Any attempts to alter course will result in immediate destruction of this vessel.

LOSIRA: Show me this unit. I wish to learn.
WATKINS: This is the matter-antimatter integrator control. That's the cut off switch.
LOSIRA: Not correct. That is the emergency overload bypass, which engages almost instantaneously. A wise precaution, considering it takes the antimatter longer to explode once the magnetic flow fails. I am for you, Mister Watkins.
WATKINS: Mister Scott, there's a strange woman who knows the entire plan of the Enterprise.

Note: A single overload bypass. Not multiple (at least two) if the m/am reactors were in the nacelles.

SCOTT: Aye, Mister Spock, and I found out why. The emergency bypass control of the matter-antimatter integrator is fused.
SCOTT: It's completely useless. The engines are running wild. There's no way to get at them. We should reach maximum overload in about fifteen minutes.

Note: Interestingly, Scotty couldn't just disengage the dilithium circuits/energisers and just cut the power to the warp engines. Perhaps if he did, then all that m/am energy has no where to go and well... boom! The M/AM engines in the nacelles are acting as the release valves until everything overloads...

SPOCK: As I recall the pattern of our fuel flow, there is an access tube leading to the matter-antimatter reaction chamber.
SCOTT: There's a service crawlway, but it's not meant to be used while the integrator operates.
SPOCK: Still, it is there, and it might be possible to shut off the fuel at that point.
SCOTT: What with? Bare hands?
SPOCK: A magnetic probe.
SCOTT: Any matter that comes in contact with antimatter triggers the explosion. And I'm not even sure a man can live in the crawlway in the energy stream of the magnetic field that bottles up the antimatter.

Note: Only one m/am reaction chamber mentioned here. And there appears to be only one place to shut off the antimatter fuel flow to it which doesn't match up with two nacelles with matter/antimatter reactors and their own antimatter fuel. Scotty would need to make a clone of himself if he were up in two different nacelles. Also, the service crawlway room wouldn't fit in the nacelle with the hallway outside.
​

and then some wiggle room to consider the possibility that the matter/antimatter reactor system consists of 3 reactor cores or chambers (1 in each nacelle and 1 in the engineering hull) that can be used individually or all together:

"Catspaw" - 30

DESALLE: Keep it up, Mister Chekov. Channel the entire output of reactors one, two, and three into the relay stations. Whatever it is, it's starting to weaken.

Note: Could indicate three matter/antimatter reactors.
​

"Galileo Seven" - 14

SCOTT: I can adjust the main reactor to function with a substitute fuel supply.
Note: This could mimic a 3 reactor setup for the Enterprise - a "main reactor" in the hull and one in each nacelle.
​

"Elaan of Troyius" - 57

SCOTT: The anti-matter pods are rigged to blow up the moment we go into warp drive.
...
SCOTT: I've got bad news, Captain. The entire dilithium crystal converter assembly is fused. No chance of repair.
SCOTT: It's completely unusable.
KIRK: No chance of restoring warp drive?
SCOTT: Not without dilithium crystals. We can't even generate enough power to fire our weapons.
...
SCOTT: Our shields will hold for a few passes, but without the matter-antimatter reactor, we've no chance. Captain, can you not call Starfleet on this emergency?
...
SPOCK: Captain, these are crude crystals. There is no way to judge what the unusual shapes will do to the energy flow.
...
SCOTT: Aye, that could blow us up just as effectively as...

Note: Scott specifies only ONE M/AM reactor but multiple antimatter pods. It is possible that the matter/antimatter reactor could contain multiple reactors (thus the multiple pods). Also with the dilithium sabotaged and no bypass available the m/am nacelles are unable to function indicating that they are dependent on some part of the energiser/dilithium machinery. Presumably the crystals need to be charged up.
​

I'll use that to segue into one of the apparent functions of the dilithium crystals in the series - they were super capacitors (or batteries) that also generated (or "regenerated") antimatter fuel:

"The Doomsday Machine" - 35

PALMER: Sir, Deck seven reports power failure in main energisers. Implementing emergency procedures. Severe casualties reported on decks three and four. Damage control party sealing off inner hull rupture.
SPOCK: It has ceased fire. We're being held in a tractor beam. We're being pulled inside, Commodore. You must veer off.
DECKER: Maintain phaser fire, helmsman.
SPOCK: We have lost warp power. If we don't break the tractor beam within sixty seconds, we never will.

Note: Warp power went when the main energisers failed and the dilithium crystals are tied to the energisers in "The Alternative Factor".
​

"The Alternative Factor" - 20

MASTERS: Whatever that phenomenon was, it drained almost all of our crystals completely. It could mean trouble.
KIRK: You have a talent for understatement, Lieutenant. Without full crystal power, our orbit will begin to decay in ten hours. Re-amplify immediately.
...
KIRK: Out of the question. Those crystals are the very heart of the power of my ship.
...
Captain's log, stardate 3088.7. We are no closer to finding an answer to the strange phenomenon than we were at the beginning. Not only have two of my crewmen been attacked, two of our dilithium crystals are missing, and without them the Enterprise cannot operate at full power. They must be found.

Note: Interestingly, not antimatter power exactly but "crystal power". This would suggest that the dilithium crystals on the Enterprise are like super capacitors or batteries that are charged up/amplified by presumably the matter/antimatter reactor. It is the dilithium energy that makes the warp propulsion go as well as generate fuel. The energisers not only provide power and fuel to the ship's systems but also act as a recharging mechanism as well. Full power means all four crystals (charged up) and/or the ability to create fuel (regenerate) at a specific rate.

LAZARUS: That's very bad, Captain. If he comes through at a time of his own choosing. But I think if we hurry and you will help me, he can yet still be stopped. There's little time left. He meant to come through. When you accidentally passed through, it drained his crystals. It'll take him about ten minutes to re-energise with the equipment aboard his ship. That should give us enough time.

Note: Lazarus uses the crystals also as a super capacitor.

SPOCK: Source of radiation, Captain.
KIRK: How is it the scanners didn't pick it up before?
SPOCK: Because it is not there.
KIRK: Another riddle? First Doctor McCoy, then you?
SPOCK: What I mean, Captain, is that according to our usual scanning procedures, there is nothing there that could be causing that effect.
KIRK: But it is there.
SPOCK: Affirmative. I confess I am somewhat at a loss for words. It may be described, though loosely and inaccurately, as a rip in our universe.
KIRK: A what?
SPOCK: A kind of physical warp, Captain, in which none of our established physical laws apply with any regularity. However, with the dilithium crystals, I was able to localise it.
LAZARUS: Yes! That's it! The dilithium crystals. With their power we could do it.

Note: Interestingly, with powered dilithium you can spot or create an opening from the antimatter universe. And when large amounts of antimatter come through from the antimatter universe the crystals are drained.
​

Note: This could go either way. The M/AM reactors in the engines at this point are sending power back to the energizers instead of creating a space warp for propulsion and now are recircuited to propulsion again. Or, the energizer is not sending power to the nacelles because they are going to the deflectors. However, the later Ep 77 "Day of the Dove" would suggest that there is M/AM in the nacelles and more than likely power was being routed down to the energizers.
​

"The Day of the Dove" - 66

SCOTT: The ship's dilithium crystals are deteriorating. We can't stop the process.
KIRK: Time factor?
SCOTT: In twelve minutes, we'll be totally without engine power.
...
SCOTT: There's no change, Captain. The dilithium crystals are discharging.

Note: Continuing evidence that the crystals store power even in a later episode.

The problem I have with that idea is that no material, by virtue of pure physics, can "store" that much energy.

Most of those lines work adequately in the sense that you define them... but most of them also work in other forms as well.

Let's just be clear... I know we all get this, but for the record... different writers had different ideas about how the Enterprise worked. These ideas are, in some cases, inherently contradictory. While your efforts are a good attempt to make it all fit, there's nothing that can make EVERYTHING fit. We have to "pick and choose" one way or the other...

Your points about the crystals "storing power" aren't really any more relevant than the idea that crystals "transform" power. In both case, the crystals are a "source of useable energy." It's just that in one case you have them "transforming and storing" while in the other case you have them merely "transforming" (and the BATTERIES are what store power).

I think "That Which Survives" is one of the absolute worst episodes of Trek, along with "The Alternative Factor" and a few others. And I'll admit that my taste for the technical stuff created by a writer is much greater when the writer wrote a story which didn't make me want to gag. But that's purely a personal perspective.

Still, there's nothing in TWS which requires there to be a single central reactor. Nothing at all. All we know is that there seems to be a single CONTROL MECHANISM. Nothing... nothing whatsoever... tells us that this control mechanism is physically attached to the reactor core(s).

People usually hear the term "antimatter integrator" and assume that this is a physical, mechanical element of the reactor core. But there is no reason to conclude that. There are elements of modern nuclear reactors which have similar nomenclature which can be miles away from the actual physical reactor cores, after all. The "reaction initiator system" in a modern reactor is basically a big hydraulic system which retracts the neutron-absorbing rods from in between the fuel rods, after all. So when I saw that episode, what I saw was the equivalent of that sort of a system.

FYI, you do make one judgement which is ENTIRELY unsupported and unsupportable. You concluded that, because a shuttlecraft explosion would leave antimatter residue, this means that the shuttlecraft is "warp powered."

Well, I do agree that shuttles have FTL capability (not necessarily "warp drive"... unlike most others, I do not treat "warp drive" and "faster than light drive" as synonyms, but rather warp drive is only one of many forms of faster-than-light propulsion). But the presence of antimatter only infers the presence of antimatter, and LIKELY of a matter/antimatter reactor.

So... if a planet has matter/antimatter reactors for planetary power, does that mean that this planet is warp-powered? I don't think so, do you?

The one thing we can take from this line is that the shuttle has antimatter aboard, likely for use in power generation (though it could be from something else as far as we know!)

The line about "reactors 1, 2 and 3" makes it clear that there are multiple reactors aboard, true... but the line wasn't "antimatter reactors 1, 2, and 3," was it?

For that matter, the idea that there are "single reactors" is not necessary supported, even in the models we've discussed. For instance, in my warp drive nacelle layout, there are four rows of reactor cylinders in each nacelle... so there are, by at least one measure, a couple of hundred "matter/antimatter reactors" (though I treat each as a subsystem, and call the whole assembly in each nacelle a single "reactor assembly").

To take this to the other side... the one I don't personally buy, mind you.. suppose that the "cathedral of tubes" is actually the reactor assembly. There are what, six rows of tube-triangles, right? Maybe this means "devote half of the output of this main reactor assembly" to the purpose you mention (leaving the remaining three reactors to their primary purposes)?

It's a mistake to assume that just because TNG has a single reactor, other ship layouts are set up that same way.

Perhaps, in TMP, each "segment" of the core we see is an individual reactor?

There are still far too many undefined variables to come to a single, unimpeachable conclusion, I'm afraid. But I do admire you for trying so hard to make everything fit... tilting at windmills, so to speak.

For me, I have my own "model" for the ship in my mind and the bits that don't match up exactly (from Elaan of Troius, mainly...) sort of get a "mental retcon."

Very little "doesn't match up" though... since I view the crystals as what turns UNUSABLE matter/antimatter reactor output into USEABLE energy. Most of EOT works just fine, with just two lines requiring a minor tweaking.

And if someone else has a totally different idea... say, a single centralized reactor... that's OK (even if I'll NEVER agree with it!). They have to reject some things, just like anyone else does. They're just rejecting bits I, personally, want to keep, and keeping bits I, personally, am more than happy to reject.

In "That Which Survives", Losira's sabotage of the engineering hull's M/AM core was enough to have a runaway ship.

Click to expand...

We don't know exactly what was sabotaged there, but the effects were on the fuel flow, and the remedy, after all the usual backups failed to be of help, was to be found in tampering with the engineering hull systems. Scotty seemed to come up with this unconventional solution on the spot, even. I'd thus say this is not specific proof either for distributed or hull-centralized systems, merely for a solution that is to be found inside the hull.

Based on this episode, nacelles in TOS may well feature antimatter, but it seems to come from the engineering hull and can be prevented from doing so by tampering with things in the engineering hull.

Note: Since the nacelles generate energy then it's a good chance they have a m/am reactor in them.

Click to expand...

A good chance, yes. But it might also be that subspace energies attract the beast, and all the nacelles do is convert, say, plasma energy to subspace energy.

Perhaps the three reactors spoken of in "Catspaw"

Click to expand...

The very fact that three are mentioned suggests there are more than three:

"Channel the entire output of reactors one, two, and three into the relay stations."

Why not "the entire output of all the reactors" if there are just three?

the dilithium crystals are tied to the energisers in "The Alternative Factor"

Click to expand...

Actually, the crystals apparently are placed in the energizers. Which might be argued to be evidence against them having anything to do with energizers normally, because they are undergoing exceptional treatment in this episode - they are being "reamplified" after having been "drained".

Are "energizers" mentioned anywhere else in TOS? In ST2, their (its?) role remains rather ill defined.

Your points about the crystals "storing power" aren't really any more relevant than the idea that crystals "transform" power. In both case, the crystals are a "source of useable energy." It's just that in one case you have them "transforming and storing" while in the other case you have them merely "transforming" (and the BATTERIES are what store power).

Click to expand...

Actually, they're pretty relevant in understanding their properties and where the crystals likely fit in the scheme of things. If they were only "transforming" then Kirk wouldn't care to re-amp them up or Lazarus wouldn't need to charge them up to open a gateway.

Still, there's nothing in TWS ["That Which Survives"] which requires there to be a single central reactor. Nothing at all. All we know is that there seems to be a single CONTROL MECHANISM. Nothing... nothing whatsoever... tells us that this control mechanism is physically attached to the reactor core(s).

Click to expand...

It's the engineering crew's dialogue that only discusses "the m/am reaction chamber". The integrator when I watched it appears to be specifically the one for the AM and near the AM fuel pod which feeds the one reactor that happens to be going wild.

I included evidence for both ways + in between and figure others can decide for themselves.

FYI, you do make one judgement which is ENTIRELY unsupported and unsupportable. You concluded that, because a shuttlecraft explosion would leave antimatter residue, this means that the shuttlecraft is "warp powered."

Click to expand...

Good catch. In my notes I had made on a different area, the shuttle (at least the one from "The Menagerie" was listed as
"ion powered" which was giving chase to the already FTL Enterprise. I'll make the change above.

There are still far too many undefined variables to come to a single, unimpeachable conclusion, I'm afraid. But I do admire you for trying so hard to make everything fit... tilting at windmills, so to speak.

Click to expand...

Thanks and as I noted above, folks mileage may vary I included my theory and data and notes for both sides of the argument plus some data that bridges both.

For me, I have my own "model" for the ship in my mind and the bits that don't match up exactly (from Elaan of Troius, mainly...) sort of get a "mental retcon."

Very little "doesn't match up" though... since I view the crystals as what turns UNUSABLE matter/antimatter reactor output into USEABLE energy. Most of EOT works just fine, with just two lines requiring a minor tweaking.

Click to expand...

FWIW, I think the theory that I have doesn't require any retcon or tweaking of the dialogue. Is there something in my theory that I missed that doesn't fit in the data that we have?

In "That Which Survives", Losira's sabotage of the engineering hull's M/AM core was enough to have a runaway ship.

Click to expand...

We don't know exactly what was sabotaged there, but the effects were on the fuel flow, and the remedy, after all the usual backups failed to be of help, was to be found in tampering with the engineering hull systems. Scotty seemed to come up with this unconventional solution on the spot, even. I'd thus say this is not specific proof either for distributed or hull-centralized systems, merely for a solution that is to be found inside the hull.

Click to expand...

I agree. However, it is data that the characters appear to focus on one reactor or "the reactor" rather than the others. Then again, it could also be argued that "the transporter room" appears to float around and one is designated as the active one "in-universe" and the characters always know which one "the transporter room" to go to. That could apply to "the reactor".

the dilithium crystals are tied to the energisers in "The Alternative Factor"

Click to expand...

Actually, the crystals apparently are placed in the energizers. Which might be argued to be evidence against them having anything to do with energizers normally, because they are undergoing exceptional treatment in this episode - they are being "reamplified" after having been "drained".

Click to expand...

Not really. First, as far as we know, the crystals were not shown to be removed from somewhere to be placed in the energizer to be re-amped. All we are shown is that the crystals are already in the energizer after Masters is told that re-amp is complete. Considering that the crystals are being constantly drained each time the Lazarus guys switch, you'd think they would be constantly be being moved to a "re-amp station" but they are not (or we don't catch them) and it doesn't appear to be a special case for them to be in the energizers. My guess is that the energizers can re-amp the crystals in place just like Lazarus' ship can charge them up once plugged in. It would've been funny if Kirk's log entry stated, "The constant universe winking phenomena is keeping the ship from using her dilithium crystals as they're constantly needing to be re-amped. Clever invasion force."

On the "Alternative Factor" issues, we do see the crystals in a location that does not correspond to the other well-known location - the articulation frame under the floor of (one of the) Main Engineering control room(s). We see a blueshirt specialist handling them. We see Kirk's ship unaffected by the repeated thefts of crystals from the energizer, whereas removing a crystal from the articulation frame appears to deprive the ship of main power.

In "Mudd's Women", the ship came equipped with six crystals, after gods know how many had been lost to the Galactic Barrier in the pilot episode. Having four crystals at a time in recuperation would keep the ship operational - so Kirk would be pretty annoyed at the repeated thefts of recently reamplified ones, but not concerned about the survival of his ship yet.

My take on this still is that dilithium needs to be in an "energized" state in order to turn antimatter into warp power, and that "energizing" and "reamplifying" may be related to the "recrystallizing" that later allows drained crystals to be nurtured back to operation. However, the energies inserted into the crystal in this manner are not the ones released for applications. Rather, the energized crystal just channels other energies - antimatter aboard the starship, but inter-universe energies (which also have something to do with antimatter, according to the dialogue) in case of the technology of the two Lazari.

On the "Alternative Factor" issues, we do see the crystals in a location that does not correspond to the other well-known location - the articulation frame under the floor of (one of the) Main Engineering control room(s).

Click to expand...

Chronologically, the "other well-known location" didn't appear until sometime in Season 2 (our POV) or much later after the "Alternative Factor". We know the engine room sections undergo modifications throughout the series so as far as we know, in "Alternative Factor" that's where the crystals go in that ship configuration, IMHO.

We see a blueshirt specialist handling them. We see Kirk's ship unaffected by the repeated thefts of crystals from the energizer, whereas removing a crystal from the articulation frame appears to deprive the ship of main power.

Click to expand...

True, but the two times this occurs in "The Alternative Factor" there are gaps in the "stealing event" where we cannot say either way if the ship exhibited a "brown out" event like we see in other episodes.

"Mudd's Women" - each time a Lithium crystal circuit failed there was a buzz and a few seconds where the lights went out. Three circuits were blown protecting Mudd's ship while the 4th on the way to the miner's planet.

"The Alternative Factor" - the first 2 Dilithium crystals that were taken we never see the removal. There is a gap where we don't know if any side effects happened or not. The 2nd time where the last 2 were taken, again there was a gap where we don't know if there was a lights out event between Kirk boarding the turbolift and when he exits.

"Paradise Syndrome" - With the ship's power cranked to full for the deflector, Scotty ejects one Dilithium to look at a fracture, causing a noticeable drop in power.

In "Mudd's Women", the ship came equipped with six crystals, after gods know how many had been lost to the Galactic Barrier in the pilot episode.

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I don't believe so. We know that in "Mudd's Women" they lost 4 crystals and it only appeared prudent for Kirk to pick up a 2 spares since he had no time to examine them. There was no indication that the ship uses 6 crystals. The Enterprise we see in "Where No Man Has Gone Before" is different from the "Mudd's Women" one since the bridge is configured differently which would suggest after the Galactic Barrier the ship underwent modifications/refit before this episode which would have brought them back up to a full crystal load. *And I don't mean a cosmetic change in the bridge. The turbolift position and main viewer position moved (depending on your viewpoint) and the forward port rail is shorter due to the change for the 2nd Pilot bridge.